Man pages for ewymathe/testALTREinstall
Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data
| ALTRE | Workflow: Post-alignment to altered enhancers and promoters |
| categAltrePeaks | Categorize altered peaks as experiment-specific,... |
| combineAnnotatePeaks | Combine and annotate peaks from different sample types.... |
| comparePeaksAltre | Comparison of methods for identifying altered regulatory... |
| countanalysis | Determines which regulatory regions are signifigantly altered... |
| enrichHeatmap | Given the output from enrichment(), creates a heatmap from... |
| getConsensusPeaks | Given a GRangeslist object with peaks for each samples,... |
| getCounts | Generates count data for regulatory regions |
| getTSS | get TSS file |
| grangestodataframe | Internal function: converts granges to dataframe |
| loadBamFiles | Read in BAM files (internal function) |
| loadBedFiles | Read in BED Files (internal function) |
| loadCSVFile | Read in CSV (internal function) |
| mergeclosepeaks | Internal function: merges peaks within user input distance of... |
| multiplot | Multiple plot function |
| pathenrich | Enrichment analysis to identify putative pathways of interest... |
| plotallvenn | Plots venn diagrams for comparison of two methods of... |
| plotCombineAnnotatePeaks | Given the output from combineAnnotatePeaks, plot a barplot... |
| plotConsensusPeaks | Given the output from getConsensusPeaks, generate a barplot... |
| plotCountAnalysis | Given the output from getCounts, plot a density plot of log2... |
| plotDistCountAnalysis | Creates a boxplot to see the distribution of read counts in... |
| plotgetcounts | Given the output from getCounts, plot a density plot of log2... |
| plotvenn | Plots a venn digram to compare sample types Plots the number... |
| rundose | Internal function: runs enrichment analysis |
| runShinyApp | run shiny app |
| statscombineannotate | Internal function: creates a stat matrix for combined and... |
| tssannotgrange | Internal function: annotates peaks as promoters or enhancers |
| writeAnnotatedRegions | Writes annotated genomic regions |
| writeBedFile | Creates a custom track for visualization on genome browser |
| writePathEnrich | Writes a data generated by pathenrich |
| writeREdf | Writes a data table generated by comparePeaksAltre |
